2-233234598-A-G

Variant names:

• chr2-233234598-A-G
• rs7563345
• ENST00000431917.5:c.-137-21504A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431917.5(ATG16L1):​c.-137-21504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,040 control chromosomes in the GnomAD database, including 30,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (30434 hom., cov: 32)
• Consequence: ATG16L1 ENST00000431917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

ATG16L1 (HGNC:21498): (autophagy related 16 like 1) The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000431917.5	c.-137-21504A>G		intron_variant	Intron 2 of 5	5		ENSP00000397512.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95787 AN: 151922 Hom.: 30410 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.630 AC: 95845 AN: 152040 Hom.: 30434 Cov.: 32 AF XY: 0.623 AC XY: 46273 AN XY: 74326

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.603

Alfa AF: 0.643 Hom.: 45108

Bravo AF: 0.626

Asia WGS AF: 0.497 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7563345; hg19: chr2-234143244;